Spatial distribution function

User discussions
1

GROMACS version: 5.1.4
GROMACS modification: Yes/No
Dear all,
I have calculated the spatial distribution function through gmx spatial command through following steps:

  1. gmx make_ndx -s a.tpr -o ou.ndx
    here ou.ndx contain the urea atoms within 0.5 nm of protein and second group is protein
  2. gmx trjconv -f a.xtc -s a.tpr -boxcenter tric -pbc none -ur compact -o b.xtc
    select 0 for system
    3.gmx trjconv -f b.xtc -s a.tpr -fit rot+trans -o c.xtc
    select 4 (backbone) for fit and output 0 for system
  3. gmx spatial -f c.xtc -s a.tpr -nab 50 -bin 0.1 -n ou.ndx
    and select urea atoms for sdf and protein for output coordinates
    but when we upload the grid.cube file in vmd as isosurface it gives output like big spehre type
    Any body can help me regarding this
2

Hi ashkan,

This result might be expected if urea is to move freely around the protein - then you might get a smoothened 0.5nm shell around the protein, which might look very much just like a big sphere.

To see more fine details, you could try to use differnet thresholds for displaying your isosurface with vmd as described here.

4

I’m with the same issue. I think that perhaps must set the reference molecule in box center with the command trjorder before spatial. Would anybody know how to use the command trjorder for fit reference molecule?

5

@ashkhan I have a problem regarding indexing that you seem to have done " urea atoms within 0.5 nm of protein" . Could you please tell how you did that. I will be thankful for your answer.

6

Check out gmx select and the selection syntax guide

Something like gmx select -on -s "resname urea and same residue as within 0.5 of protein"

That syntax guide has good examples.